Methods for Analysis of Nanopore DNA Sequencing Data.

摘要

Technology guides the practice of scientific inquiry. In the biological sciences, DNA sequencing has encouraged the commingling of traditional experimental biology and computer science. In this thesis, I describe computational and biochemical methods for DNA sequencing technology. Nanopore DNA sequencing is an single-molecule technology that shows promise in the area of read lengths, instrument portability, and, as shown in this work, chemical modification detection. A nanopore sequencing device contains a nanometer-sized pore that separates two electrolyte buffer reservoirs. A voltage potential is applied across the nanopore and the device records the ionic current through pore. As DNA polymers translocate through the pore they modulate the ionic current by partially obstructing the pore in a sequence-dependent manner. In Chapter 2 I describe a hidden Markov model for the nanopore ionic current and how a hierarchical Dirichlet process can be used to model new non-canonical (modified) bases affording a HMM-HDP model. In chapter 3 I show how the model can detect multiple chemical modifications to DNA. The last section of the paper describes a biochemical method to re-read DNA sequences using a nanopore and a helicase enzyme.